#!/usr/bin/perl #print this MIME data no matter what print "Content-type: text/html\n\n"; #flush stdout buffer $| = 1; &parse_form_data (*data); #Calculations use Table; $loc_data_table = "features"; $scid = $data{'scid'}; $scid =~ s/^\s*(.*?)\s*$/$1/; #get rid of bordering white space $scid = uc($scid); $scid =~ s/-//g; #remove any hyphens from scid $opt = $data{'opt'}; #first see if the id format is correct foreach (T_LoadRows ($loc_data_table)) { if ($_->{"scid_"} eq $scid) { ($cdc28) = T_GetFields($_,"cdc28"); ($masageg,$masagel,$masages,$mayoung,$ch_a,$ch_alpha,$ch_gal,$ch_heat,$samson,$mrcyc15,$mrcyc28,$mrcycsd,$mrcyelu,$mrdiasd,$cdc28,$ckii,$coildco,$farn,$ggsi,$glyc,$hdel,$knocout,$length,$mit1,$mit2,$myri,$nuc1,$nuc2,$pi,$pka,$plmnew1,$pox1,$rostall,$sig1,$signalp,$tms1,$ref_mrna_expr,$ref_prot_expr) = T_GetFields($_,"sage-gm_phase","sage-l_phase","sage-s_phase","young","church-a","church-alpha","church-gal","church-heat","samson","std-cdc15","std-cdc28","std-alpha","std-elu","std-diauxic","cdc28","ckii","coildco","farn","ggsi","glyc","hdel","knockout","length","mit1","mit2","myri","nuc1","nuc2","pi","pka","plmnew1","pox1","rostall","sig1","signalp","tms1","ref_mrna_expr","ref_prot_expr"); last; } } if (not defined $cdc28){ #ORF not found print "The ORF you specified does not exist."; exit(1); } if ($knocout == 1) {$knocout = "lethal";} else {$knocout = "viable";} ############################################################################### #CGI Output #Create html document print < ORF Features HTML my $hvar = `perl /web/genecensus/header/header.cgi features`; print $hvar; print <Features for $scid
Absolute Expression Data
FeatureValue
Reference mRNA Expression (copies/cell) $ref_mrna_expr
Reference Protein Expression (10^3 copies/cell) $ref_prot_expr
Young mRNA Expression [Help] $mayoung
SAGE mRNA Expression (g/m phase) [Help] $masageg
SAGE mRNA Expression (l phase) [Help] $masagel
SAGE mRNA Expression (s phase) [Help] $masages
Church mRNA Expression (a) [Help] $ch_a
Church mRNA Expression (alpha) [Help] $ch_alpha
Church mRNA Expression (gal) [Help] $ch_gal
Church mRNA Expression (heat) [Help] $ch_heat
Samson mRNA Expression [Help] $samson
Relative Expression Data
FeatureValue
Cell Cycle mRNA Expr. Fluctuation (CDC15 arrest) [Help] $mrcyc15
Cell Cycle mRNA Expr. Fluctuation (CDC28 arrest) [Help] $mrcyc28
Cell Cycle mRNA Expr. Fluctuation (Alpha-factor arrest) [Help] $mrcycsd
Cell Cycle mRNA Expr. Fluctuation (Elutriation) [Help] $mrcyelu
Diauxic Shift mRNA Expr. Fluctuation [Help] $mrdiasd
Sequence Motifs
FeatureValue
Nuclear Localization Signal 1 [Help] $nuc1
Nuclear Localization Signal 2 [Help] $nuc2
Mitochondrial Signal 1 [Help] $mit1
Mitochondrial Signal 2 [Help] $mit2
HDEL ER Retention Signal [Help] $hdel
Plasma Membrane Signal [Help] $plmnew1
Peroxisome Import Signal [Help] $pox1
Signal Sequence (method 1) [Help] $sig1
Signal Sequence (method 2) [Help] $signalp
Glycosylation sites [Help] $glyc
Farnesylation site [Help] $farn
Geranylgeranylation site [Help] $ggsi
Myristolation site [Help] $myri HTML if ($opt =~ /1/) { print <Potential CDC 28 kinase sites [Help] $cdc28
Potential Casein kinase II sites [Help] $ckii HTML } print <Potential protein kinase A target sites [Help] $pka
Coiled Coils [Help] $coildco
Other Properties
FeatureValue
Knockout Mutation [Help] $knocout
Isoelectric Point [Help] $pi
Trans-membrane Segments [Help] $tms1
Length (amino acids) [Help] $length
Surface Amino Acid Composition Compartment [Help] $rostall


HTML exit; sub parse_form_data { local (*FORM_DATA) = @_; local ($request_method, $query_string, @key_value_pairs, $key_value, $key, $value); $request_method = $ENV{'REQUEST_METHOD'}; if ($request_method eq "GET") { $query_string = $ENV{'QUERY_STRING'}; } elsif ($request_method eq "POST") { read(STDIN, $query_string, $ENV{'CONTENT_LENGTH'}); #no. of bytes to receive } else { &return_error (500, "Server Error", "Server uses unsupported method"); } @pairs = split(/&/, $query_string); #making list of keyword-value pair foreach $pair (@pairs) { ($key, $value) = split(/=/, $pair); $value =~ tr/+/ /; #translate "+" to space #decipher ASCI hexadecimal escaped characters $value =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C", hex($1))/eg; if (defined ($FORM_DATA{$key})) { $FORM_DATA{$key} = join ("\0", $FORM_DATA{$key}, $value); } else { $FORM_DATA{$key} = $value; } } } sub return_error { local ($status, $keyword, $message) = @_; print "Content-type: text/html", "\n"; print "Status: ", $status, " ", $keyword, "\n\n"; print < CGI Program - Unexpected Error

$keyword

$message
Please contact the webmaster for more information. End_of_Error exit(1); }